Sequence
atgc intronic sequence ATGC exonic sequence...aattaaaccaaattaattttgctagttaattactaccactcttcttcaattcagccactgtggattaattactttactgaaattttgactgaaacgacagGCTTACATCCAGCAGCTGGAGTCCAGCAGGATCAGGCTTGCTCAGCTCGAACAGGAACTGCACACCGCGAGAGCCCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os09g31390.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g31390.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G006578_T01 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------------------------------aattaaaccaaattaattttgcta--gtt--aattactaccactcttcttcaattcagccactgtggattaat--tactttactgaaattttgactgaaacgacagGCTTACATCCAGCAGCTGGAGTCCAGCAGGATCAGGCTTGCTCAGCTCGAACAGGAACTGCACACCGCGAGAGCCCAG
|| | || |||| | ||| |||| | | | | |||| | || ||| |||| || | |||||| ||||| | | |||||||||||||||||| || ||||||||||||||||| || |||||||||||||| ||||||||||| || ||||| |||
gtgagcgagtctcgatactgatgacctacatcaagattggaacaaaagaacgagaaaaaatataatggcaaagagttaacatcgttttctttgttttttttgaagtttgacatggttcaaattcttgtctccaccatccaat---gacagtgtagatttatattgttttacttctcttttgctgcatgcaacagGCTTACATCCAGCAACTCGAGTCCAGCAGGATCAGACTAGCTCAGCTCGAACAAGAACTGCACACTGCAAGAGCTCAG
upper sequence: LOC_Os09g31390.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G125934_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------------------------------------aattaaaccaaattaattttgctagttaattactaccactc------ttcttcaattcagccactgtggattaa---ttactttactgaaattttgactgaaacg---acagGCTTACATCCAGCAGCTGGAGTCCAGCAGGATCAGGCTTGCTCAGCTCGAACAGGAACTGCACACCGCGAGAGCCCAG---
|| || | |||||| | || || || ||| || || | | ||| ||| ||| | | ||| |||||| || |||| || | |||||||||||||||||| || |||||||||||||||||||| |||||||||||||| ||||| ||||| | ||||| ||
gtgagtgagtcgacagctgatgacctacaaaggctacaccatgatttgaacagaaacgagtagaaaaaaatgacaaagaattaacattaatccttttaatttcttgatactgttcaaattattgtccctatcatccaatgtcaacgcagatttattttacttctcttcacactgtaatgcaaacagGCTTACATCCAGCAACTCGAGTCCAGCAGGATCAGGCTAGCTCAGCTCGAACAAGAACTTCACACTACAAGAGCTCATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaattcagccactgtggattaattactttactgaaattttgactgaaacgacagGCTTACATCCAGCAGCTGGAGTCCAGCAGGATCAGGCTTGCTCAGCTCGAACAGGAACTGCACACCGCGAGAGCCCAG
ttttgac putative branch site (score: 3)
attaattactttactg TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattaaaccaaattaattttgctagttaattactaccactcttcttcaattcagccactgtggattaattactttactgaaattttgactgaaacgacagGCTTACATCCAGCAGCTGGAGTCCAGCAGGATCAGGCTTGCTCAGCTCGAACAGGAACTGCACACCGCGAGAGCCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - aaaccaa
- - - - - - - - ttttgct
- - - - - - - - - - - - - - - - ctaccac
- - - - - - - - - - - - - - - - - - - - - - - - - - -gccactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttactga